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Li M, Li D, Lu M, Mo S, Ding S, Chen Y, Lai Y, Zhang D, Liao W, Fan Q. A new species of Cotoneaster (Rosaceae) from western Sichuan, China. PHYTOKEYS 2023; 236:39-52. [PMID: 38058313 PMCID: PMC10696602 DOI: 10.3897/phytokeys.236.111819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
Cotoneasterdensiflorus, a new species of Rosaceae from western Sichuan, China, is described and illustrated. Morphologically, we inferred that the new species belongs to CotoneasterSer.Salicifolii sensu Yü et al. (1974) in the Flora of China and Fryer and Hylmö (2009). This species is most similar to C.salicifolius, but differs in its leaf blade of ovate-lanceolate to obovate shape (vs. elliptic-oblong to ovate-lanceolate), smaller length-width ratio of 2.37 ± 0.31 (vs. 3.17 ± 0.32), slightly conduplicate (vs. not conduplicate), less lateral veins of 6-8 pairs (vs. 12-16 pairs), upper surface slightly rugose (vs. rugose), leaf margin plane (vs. revolute), lower surface densely grey tomentose (vs. grey tomentose, with bloom), greater corolla diameter of 7-9 mm (vs. 5-6 mm), styles 2 (vs. 2-3), pyrenes 2 (vs. 2-3), larger pollen grains P/E values of 2.05 ± 0.12 (vs. 1.19 ± 0.05) and leaf epidermis type W (vs. type I). Based on phylogenetic analysis of the whole chloroplast genome, C.densiflorus is sister to C.rhytidophyllus, but distantly related to C.salicifolius.
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Affiliation(s)
- Mingwan Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Agricultural UniversityZhengzhouChina
| | - Dan Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Agricultural UniversityZhengzhouChina
| | - Mengfei Lu
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Agricultural UniversityZhengzhouChina
| | - Shuangfeng Mo
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Agricultural UniversityZhengzhouChina
| | - Shen Ding
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Agricultural UniversityZhengzhouChina
| | - Yuanyuan Chen
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Agricultural UniversityZhengzhouChina
| | - Yong Lai
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Agricultural UniversityZhengzhouChina
| | - Dangquan Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Agricultural UniversityZhengzhouChina
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, ChinaSun Yat-sen UniversityGuangzhouChina
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, ChinaSun Yat-sen UniversityGuangzhouChina
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Infrageneric Plastid Genomes of Cotoneaster (Rosaceae): Implications for the Plastome Evolution and Origin of C. wilsonii on Ulleung Island. Genes (Basel) 2022; 13:genes13050728. [PMID: 35627113 PMCID: PMC9141645 DOI: 10.3390/genes13050728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 12/31/2022] Open
Abstract
Cotoneaster is a taxonomically and ornamentally important genus in the family Rosaceae; however, phylogenetic relationships among its species are complicated owing to insufficient morphological diagnostic characteristics and hybridization associated with polyploidy and apomixis. In this study, we sequenced the complete plastomes of seven Cotoneaster species (C. dielsianus, C. hebephyllus, C. integerrimus, C. mongolicus, C. multiflorus, C. submultiflorus, and C. tenuipes) and included the available complete plastomes in a phylogenetic analysis to determine the origin of C. wilsonii, which is endemic to Ulleung Island, Korea. Furthermore, based on 15 representative lineages within the genus, we carried out the first comparative analysis of Cotoneaster plastid genomes to gain an insight into their molecular evolution. The plastomes were highly conserved, with sizes ranging from 159,595 bp (C. tenuipes) to 160,016 bp (C. hebephyllus), and had a GC content of 36.6%. The frequency of codon usage showed similar patterns among the 15 Cotoneaster species, and 24 of the 35 protein-coding genes were predicted to undergo RNA editing. Eight of the 76 common protein-coding genes, including ccsA, matK, ndhD, ndhF, ndhK, petA, rbcL, and rpl16, were positively selected, implying their potential roles in adaptation and speciation. Of the 35 protein-coding genes, 24 genes (15 photosynthesis-related, seven self-replications, and three others) were found to harbor RNA editing sites. Furthermore, several mutation hotspots were identified, including trnG-UCC/trnR-UCU/atpA and trnT-UGU/trnL-UAA. Maximum likelihood analysis based on 57 representative plastomes of Cotoneaster and two Heteromeles plastomes as outgroups revealed two major lineages within the genus, which roughly correspond to two subgenera, Chaenopetalum and Cotoneaster. The Ulleung Island endemic, C. wilsonii, shared its most recent common ancestor with two species, C. schantungensis and C. zabelii, suggesting its potential origin from geographically close members of the subgenus Cotoneaster, section Integerrimi.
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Genome Size, Cytotype Diversity and Reproductive Mode Variation of Cotoneaster integerrimus (Rosaceae) from the Balkans. PLANTS 2021; 10:plants10122798. [PMID: 34961270 PMCID: PMC8708406 DOI: 10.3390/plants10122798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/28/2022]
Abstract
Cotoneaster integerrimus represents a multiploid and facultative apomictic system of widely distributed mountain populations. We used flow cytometry to determine genome size, ploidy level, and reproduction mode variation of the Balkan populations, supplemented by analysis of nuclear microsatellites in order to address: (i) geographic distribution and variation of cytotypes among the populations; (ii) variation of reproduction mode and the frequency of sexuality; (iii) pathways of endosperm formation among the sampled polyploids and their endosperm balance requirements; (iv) genotypic diversity and geographic distribution of clonal lineages of polyploids. The prevalence of apomictic tetraploid cytotype followed by sexual diploids and extremely rare triploids was demonstrated. This prevalence of tetraploids affected the populations’ structure composed from clonal genotypes with varying proportions. The co-occurrence of diploids and tetraploids generated higher cytotype, reproductive mode, and genotypic diversity, but mixed-ploidy sites were extremely rare. The endosperm imbalance facilitates the development and the occurrence of intermediate triploids in mixed-ploidy populations, but also different tetraploid lineages elsewhere with unbalanced endosperm. All these results showed that the South European populations of C. integerrimus have higher levels of cytotype and reproductive diversity compared to the Central European ones. Therefore, the South European populations can be considered as a potential reservoir of regional and global diversity for this species.
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Chen S, Milne R, Zhou R, Meng K, Yin Q, Guo W, Ma Y, Mao K, Xu K, Kim YD, Do TV, Liao W, Fan Q. When tropical and subtropical congeners met: Multiple ancient hybridization events within Eriobotrya in the Yunnan-Guizhou Plateau, a tropical-subtropical transition area in China. Mol Ecol 2021; 31:1543-1561. [PMID: 34910340 DOI: 10.1111/mec.16325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 01/09/2023]
Abstract
Global climate changes during the Miocene may have created ample opportunities for hybridization between members of tropical and subtropical biomes at the boundary between these zones. Yet, very few studies have explored this possibility. The Yunnan-Guizhou Plateau (YGP) in Southwest China is a biodiversity hotspot for vascular plants, located in a transitional area between the floristic regions of tropical Southeast Asia and subtropical East Asia. The genus Eriobotrya (Rosaceae) comprises both tropical and subtropical taxa, with 12 species recorded in the YGP, making it a suitable basis for testing the hypothesis of between-biome hybridization. Therefore, we surveyed the evolutionary history of Eriobotrya by examining three chloroplast regions and five nuclear genes for 817 individuals (47 populations) of 23 Eriobotrya species (including 19 populations of 12 species in the YGP), plus genome re-sequencing of 33 representative samples. We concluded that: (1) phylogenetic positions for 16 species exhibited strong cytonuclear conflicts, most probably due to ancient hybridization; (2) the YGP is a hotspot for hybridization, with 11 species showing clear evidence of chloroplast capture; and (3) Eriobotrya probably originated in tropical Asia during the Eocene. From the Miocene onwards, the intensification of the Eastern Asia monsoon and global cooling may have shifted the tropical-subtropical boundary and caused secondary contact between species, thus providing ample opportunity for hybridization and diversification of Eriobotrya, especially in the YGP. Our study highlights the significant role that paleoclimate changes probably played in driving hybridization and generating rich species diversity in climate transition zones.
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Affiliation(s)
- Sufang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Richard Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Kaikai Meng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qianyi Yin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Guo
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongpeng Ma
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Kewang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Young-Dong Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon City, South Korea
| | - Truong Van Do
- Vietnam National Museum of Nature, Vietnam Academy of Science & Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science & Technology, Hanoi, Vietnam
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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Liston A, Weitemier KA, Letelier L, Podani J, Zong Y, Liu L, Dickinson TA. Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization. PeerJ 2021; 9:e12418. [PMID: 34754629 PMCID: PMC8555502 DOI: 10.7717/peerj.12418] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/10/2021] [Indexed: 11/20/2022] Open
Abstract
Background Hawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups. Methods We used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies. Results We obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridization in the evolution of Crataegus. Hybridization between subgenus Americanae and subgenus Sanguineae was documented for the origin of Sanguineae tetraploids, but not for a tetraploid Americanae species. This is also the first application of target capture probes designed with apple genome sequence. We successfully assembled 95% of 257 loci in Crataegus, indicating their potential utility across the genera of the apple tribe.
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Affiliation(s)
- Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Kevin A Weitemier
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America.,Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
| | - Lucas Letelier
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - János Podani
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Lorand University, Budapest, Hungary
| | - Yu Zong
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America.,College of Chemistry & Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Lang Liu
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Timothy A Dickinson
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Lyu R, He J, Luo Y, Lin L, Yao M, Cheng J, Xie L, Pei L, Yan S, Li L. Natural Hybrid Origin of the Controversial "Species" Clematis × pinnata (Ranunculaceae) Based on Multidisciplinary Evidence. FRONTIERS IN PLANT SCIENCE 2021; 12:745988. [PMID: 34712260 PMCID: PMC8545901 DOI: 10.3389/fpls.2021.745988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/22/2021] [Indexed: 05/23/2023]
Abstract
Interspecific hybridization is common and has often been viewed as a driving force of plant diversity. However, it raises taxonomic problems and thus impacts biodiversity estimation and biological conservation. Although previous molecular phylogenetic studies suggested that interspecific hybridization may be rather common in Clematis, and artificial hybridization has been widely applied to produce new Clematis cultivars for nearly two centuries, the issue of natural hybridization of Clematis has never been addressed in detail. In this study, we tested the hybrid origin of a mesophytic and cold-adapted vine species, Clematis pinnata, which is a rare and taxonomically controversial taxon endemic to northern China. Using field investigations, flow cytometry (FCM), phylogenomic analysis, morphological statistics, and niche modeling, we tested hybrid origin and species status of C. pinnata. The FCM results showed that all the tested species were homoploid (2n = 16). Phylonet and HyDe analyses based on transcriptome data showed the hybrid origins of C. × pinnata from either C. brevicaudata × C. heracleifolia or C. brevicaudata × C. tubulosa. The plastome phylogeny depicted that C. × pinnata in different sampling sites originated by different hybridization events. Morphological analysis showed intermediacy of C. × pinnata between its putative parental species in many qualitative and quantitative characters. Niche modeling results suggested that C. × pinnata had not been adapted to a novel ecological niche independent of its putative parents. These findings demonstrated that plants of C. × pinnata did not formed a self-evolved clade and should not be treated as a species. The present study also suggests that interspecific hybridization is a common mechanism in Clematis to generate diversity and variation, and it may play an important role in the evolution and diversification of this genus. Our study implies that morphological diversity caused by natural hybridization may overstate the real species diversity in Clematis.
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Affiliation(s)
- Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Lele Lin
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Min Yao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Linying Pei
- Beijing Engineering Research Center for Landscape Plant, Beijing Forestry University Forest Science Co. Ltd., Beijing, China
| | - Shuangxi Yan
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Liangqian Li
- Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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Grabenstein KC, Taylor SA. Breaking Barriers: Causes, Consequences, and Experimental Utility of Human-Mediated Hybridization. Trends Ecol Evol 2018; 33:198-212. [DOI: 10.1016/j.tree.2017.12.008] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 11/08/2017] [Accepted: 12/12/2017] [Indexed: 12/21/2022]
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